Riley R

References (20)

Title : Comprehensive genomic and transcriptomic analysis of polycyclic aromatic hydrocarbon degradation by a mycoremediation fungus, Dentipellis sp. KUC8613 - Park_2019_Appl.Microbiol.Biotechnol_103_8145
Author(s) : Park H , Min B , Jang Y , Kim J , Lipzen A , Sharma A , Andreopoulos B , Johnson J , Riley R , Spatafora JW , Henrissat B , Kim KH , Grigoriev IV , Kim JJ , Choi IG
Ref : Applied Microbiology & Biotechnology , 103 :8145 , 2019
Abstract : The environmental accumulation of polycyclic aromatic hydrocarbons (PAHs) is of great concern due to potential carcinogenic and mutagenic risks, as well as their resistance to remediation. While many fungi have been reported to break down PAHs in environments, the details of gene-based metabolic pathways are not yet comprehensively understood. Specifically, the genome-scale transcriptional responses of fungal PAH degradation have rarely been reported. In this study, we report the genomic and transcriptomic basis of PAH bioremediation by a potent fungal degrader, Dentipellis sp. KUC8613. The genome size of this fungus was 36.71 Mbp long encoding 14,320 putative protein-coding genes. The strain efficiently removed more than 90% of 100 mg/l concentration of PAHs within 10 days. The genomic and transcriptomic analysis of this white rot fungus highlights that the strain primarily utilized non-ligninolytic enzymes to remove various PAHs, rather than typical ligninolytic enzymes known for playing important roles in PAH degradation. PAH removal by non-ligninolytic enzymes was initiated by both different PAH-specific and common upregulation of P450s, followed by downstream PAH-transforming enzymes such as epoxide hydrolases, dehydrogenases, FAD-dependent monooxygenases, dioxygenases, and glycosyl- or glutathione transferases. Among the various PAHs, phenanthrene induced a more dynamic transcriptomic response possibly due to its greater cytotoxicity, leading to highly upregulated genes involved in the translocation of PAHs, a defense system against reactive oxygen species, and ATP synthesis. Our genomic and transcriptomic data provide a foundation of understanding regarding the mycoremediation of PAHs and the application of this strain for polluted environments.
ESTHER : Park_2019_Appl.Microbiol.Biotechnol_103_8145
PubMedSearch : Park_2019_Appl.Microbiol.Biotechnol_103_8145
PubMedID: 31482283
Gene_locus related to this paper: 9agam-a0a5b1qnb8 , 9agam-a0a5b1qwq3 , 9agam-a0a5b1qh04 , 9agam-a0a5b1qyk1 , 9agam-a0a5b1qmi3 , 9agam-a0a5b1qi91 , 9agam-a0a5b1qhi2

Title : Megaphylogeny resolves global patterns of mushroom evolution - Varga_2019_Nat.Ecol.Evol_3_668
Author(s) : Varga T , Krizsan K , Foldi C , Dima B , Sanchez-Garcia M , Sanchez-Ramirez S , Szollosi GJ , Szarkandi JG , Papp V , Albert L , Andreopoulos W , Angelini C , Antonin V , Barry KW , Bougher NL , Buchanan P , Buyck B , Bense V , Catcheside P , Chovatia M , Cooper J , Damon W , Desjardin D , Finy P , Geml J , Haridas S , Hughes K , Justo A , Karasinski D , Kautmanova I , Kiss B , Kocsube S , Kotiranta H , LaButti KM , Lechner BE , Liimatainen K , Lipzen A , Lukacs Z , Mihaltcheva S , Morgado LN , Niskanen T , Noordeloos ME , Ohm RA , Ortiz-Santana B , Ovrebo C , Racz N , Riley R , Savchenko A , Shiryaev A , Soop K , Spirin V , Szebenyi C , Tomsovsky M , Tulloss RE , Uehling J , Grigoriev IV , Vagvolgyi C , Papp T , Martin FM , Miettinen O , Hibbett DS , Nagy LG
Ref : Nat Ecol Evol , 3 :668 , 2019
Abstract : Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with the spread of (sub)tropical coniferous forests and a warming climate. A possible mass extinction, several clade-specific adaptive radiations and morphological diversification of fruiting bodies followed during the Cretaceous and the Paleogene, convergently giving rise to the classic toadstool morphology, with a cap, stalk and gills (pileate-stipitate morphology). This morphology is associated with increased rates of lineage diversification, suggesting it represents a key innovation in the evolution of mushroom-forming fungi. The increase in mushroom diversity started during the Mesozoic-Cenozoic radiation event, an era of humid climate when terrestrial communities dominated by gymnosperms and reptiles were also expanding.
ESTHER : Varga_2019_Nat.Ecol.Evol_3_668
PubMedSearch : Varga_2019_Nat.Ecol.Evol_3_668
PubMedID: 30886374
Gene_locus related to this paper: 9aphy-a0a5c3ppg9 , 9aphy-a0a371d1b5 , 9agam-a0a5c3ngv5 , 9aphy-a0a5c3nsu3 , 9agar-a0a4s8mrh7 , 9agar-a0a4s8mil0

Title : Genomics and Development of Lentinus tigrinus: A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies - Wu_2018_Genome.Biol.Evol_10_3250
Author(s) : Wu B , Xu Z , Knudson A , Carlson A , Chen N , Kovaka S , LaButti K , Lipzen A , Pennachio C , Riley R , Schakwitz W , Umezawa K , Ohm RA , Grigoriev IV , Nagy LG , Gibbons J , Hibbett D
Ref : Genome Biol Evol , 10 :3250 , 2018
Abstract : Lentinus tigrinus is a species of wood-decaying fungi (Polyporales) that has an agaricoid form (a gilled mushroom) and a secotioid form (puffball-like, with enclosed spore-bearing structures). Previous studies suggested that the secotioid form is conferred by a recessive allele of a single locus. We sequenced the genomes of one agaricoid (Aga) strain and one secotioid (Sec) strain (39.53-39.88 Mb, with 15,581-15,380 genes, respectively). We mated the Sec and Aga monokaryons, genotyped the progeny, and performed bulked segregant analysis (BSA). We also fruited three Sec/Sec and three Aga/Aga dikaryons, and sampled transcriptomes at four developmental stages. Using BSA, we identified 105 top candidate genes with nonsynonymous SNPs that cosegregate with fruiting body phenotype. Transcriptome analyses of Sec/Sec versus Aga/Aga dikaryons identified 907 differentially expressed genes (DEGs) along four developmental stages. On the basis of BSA and DEGs, the top 25 candidate genes related to fruiting body development span 1.5 Mb (4% of the genome), possibly on a single chromosome, although the precise locus that controls the secotioid phenotype is unresolved. The top candidates include genes encoding a cytochrome P450 and an ATP-dependent RNA helicase, which may play a role in development, based on studies in other fungi.
ESTHER : Wu_2018_Genome.Biol.Evol_10_3250
PubMedSearch : Wu_2018_Genome.Biol.Evol_10_3250
PubMedID: 30398645
Gene_locus related to this paper: 9aphy-a0a5c2t2q2

Title : Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass - Miyauchi_2018_Biotechnol.Biofuels_11_201
Author(s) : Miyauchi S , Rancon A , Drula E , Hage H , Chaduli D , Favel A , Grisel S , Henrissat B , Herpoel-Gimbert I , Ruiz-Duenas FJ , Chevret D , Hainaut M , Lin J , Wang M , Pangilinan J , Lipzen A , Lesage-Meessen L , Navarro D , Riley R , Grigoriev IV , Zhou S , Raouche S , Rosso MN
Ref : Biotechnol Biofuels , 11 :201 , 2018
Abstract : Background: Plant biomass conversion for green chemistry and bio-energy is a current challenge for a modern sustainable bioeconomy. The complex polyaromatic lignin polymers in raw biomass feedstocks (i.e., agriculture and forestry by-products) are major obstacles for biomass conversions. White-rot fungi are wood decayers able to degrade all polymers from lignocellulosic biomass including cellulose, hemicelluloses, and lignin. The white-rot fungus Polyporus brumalis efficiently breaks down lignin and is regarded as having a high potential for the initial treatment of plant biomass in its conversion to bio-energy. Here, we describe the extraordinary ability of P. brumalis for lignin degradation using its enzymatic arsenal to break down wheat straw, a lignocellulosic substrate that is considered as a biomass feedstock worldwide. Results: We performed integrative multi-omics analyses by combining data from the fungal genome, transcriptomes, and secretomes. We found that the fungus possessed an unexpectedly large set of genes coding for Class II peroxidases involved in lignin degradation (19 genes) and GMC oxidoreductases/dehydrogenases involved in generating the hydrogen peroxide required for lignin peroxidase activity and promoting redox cycling of the fungal enzymes involved in oxidative cleavage of lignocellulose polymers (36 genes). The examination of interrelated multi-omics patterns revealed that eleven Class II Peroxidases were secreted by the fungus during fermentation and eight of them where tightly co-regulated with redox cycling enzymatic partners. Conclusion: As a peculiar feature of P. brumalis, we observed gene family extension, up-regulation and secretion of an abundant set of versatile peroxidases and manganese peroxidases, compared with other Polyporales species. The orchestrated secretion of an abundant set of these delignifying enzymes and redox cycling enzymatic partners could contribute to the delignification capabilities of the fungus. Our findings highlight the diversity of wood decay mechanisms present in Polyporales and the potentiality of further exploring this taxonomic order for enzymatic functions of biotechnological interest.
ESTHER : Miyauchi_2018_Biotechnol.Biofuels_11_201
PubMedSearch : Miyauchi_2018_Biotechnol.Biofuels_11_201
PubMedID: 30061923
Gene_locus related to this paper: 9aphy-a0a371d1b5 , 9aphy-a0a371dju9

Title : Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria - Sipos_2017_Nat.Ecol.Evol_1_1931
Author(s) : Sipos G , Prasanna AN , Walter MC , O'Connor E , Balint B , Krizsan K , Kiss B , Hess J , Varga T , Slot J , Riley R , Boka B , Rigling D , Barry K , Lee J , Mihaltcheva S , LaButti K , Lipzen A , Waldron R , Moloney NM , Sperisen C , Kredics L , Vagvolgyi C , Patrignani A , Fitzpatrick D , Nagy I , Doyle S , Anderson JB , Grigoriev IV , Guldener U , Munsterkotter M , Nagy LG
Ref : Nat Ecol Evol , 1 :1931 , 2017
Abstract : Armillaria species are both devastating forest pathogens and some of the largest terrestrial organisms on Earth. They forage for hosts and achieve immense colony sizes via rhizomorphs, root-like multicellular structures of clonal dispersal. Here, we sequenced and analysed the genomes of four Armillaria species and performed RNA sequencing and quantitative proteomic analysis on the invasive and reproductive developmental stages of A. ostoyae. Comparison with 22 related fungi revealed a significant genome expansion in Armillaria, affecting several pathogenicity-related genes, lignocellulose-degrading enzymes and lineage-specific genes expressed during rhizomorph development. Rhizomorphs express an evolutionarily young transcriptome that shares features with the transcriptomes of both fruiting bodies and vegetative mycelia. Several genes show concomitant upregulation in rhizomorphs and fruiting bodies and share cis-regulatory signatures in their promoters, providing genetic and regulatory insights into complex multicellularity in fungi. Our results suggest that the evolution of the unique dispersal and pathogenicity mechanisms of Armillaria might have drawn upon ancestral genetic toolkits for wood-decay, morphogenesis and complex multicellularity.
ESTHER : Sipos_2017_Nat.Ecol.Evol_1_1931
PubMedSearch : Sipos_2017_Nat.Ecol.Evol_1_1931
PubMedID: 29085064
Gene_locus related to this paper: armos-armb

Title : Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus - de Vries_2017_Genome.Biol_18_28
Author(s) : de Vries RP , Riley R , Wiebenga A , Aguilar-Osorio G , Amillis S , Uchima CA , Anderluh G , Asadollahi M , Askin M , Barry K , Battaglia E , Bayram O , Benocci T , Braus-Stromeyer SA , Caldana C , Canovas D , Cerqueira GC , Chen F , Chen W , Choi C , Clum A , Dos Santos RA , Damasio AR , Diallinas G , Emri T , Fekete E , Flipphi M , Freyberg S , Gallo A , Gournas C , Habgood R , Hainaut M , Harispe ML , Henrissat B , Hilden KS , Hope R , Hossain A , Karabika E , Karaffa L , Karanyi Z , Krasevec N , Kuo A , Kusch H , LaButti K , Lagendijk EL , Lapidus A , Levasseur A , Lindquist E , Lipzen A , Logrieco AF , Maccabe A , Makela MR , Malavazi I , Melin P , Meyer V , Mielnichuk N , Miskei M , Molnar AP , Mule G , Ngan CY , Orejas M , Orosz E , Ouedraogo JP , Overkamp KM , Park HS , Perrone G , Piumi F , Punt PJ , Ram AF , Ramon A , Rauscher S , Record E , Riano-Pachon DM , Robert V , Rohrig J , Ruller R , Salamov A , Salih NS , Samson RA , Sandor E , Sanguinetti M , Schutze T , Sepcic K , Shelest E , Sherlock G , Sophianopoulou V , Squina FM , Sun H , Susca A , Todd RB , Tsang A , Unkles SE , van de Wiele N , van Rossen-Uffink D , Oliveira JV , Vesth TC , Visser J , Yu JH , Zhou M , Andersen MR , Archer DB , Baker SE , Benoit I , Brakhage AA , Braus GH , Fischer R , Frisvad JC , Goldman GH , Houbraken J , Oakley B , Pocsi I , Scazzocchio C , Seiboth B , vanKuyk PA , Wortman J , Dyer PS , Grigoriev IV
Ref : Genome Biol , 18 :28 , 2017
Abstract : BACKGROUND: The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. RESULTS: We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. CONCLUSIONS: Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.
ESTHER : de Vries_2017_Genome.Biol_18_28
PubMedSearch : de Vries_2017_Genome.Biol_18_28
PubMedID: 28196534
Gene_locus related to this paper: asptu-a0a1l9nhd0 , aspve-a0a1l9pxx8 , aspve-a0a1l9q4m3 , aspwe-a0a1l9s133 , 9euro-a0a1l9t3v9 , aspwe-a0a1l9rcx6 , aspna-g3y5a6 , aspgl-a0a1l9v4d3 , 9euro-a0a1l9sa36 , aspsb-a0a319eji6 , aspve-a0a1l9px96 , 9euro-a0a1l9tay1 , aspgl-a0a1l9vbc0 , aspc5-a0a1r3rh65 , 9euro-a0a2v5i956 , aspwe-a0a1l9rpp6 , aspna-g3xpw9 , aspve-a0a1l9plv1 , 9euro-a0a1l9tk47 , aspve-a0a1l9pde9 , aspve-a0a1l9pz72 , aspwe-a0a1l9rde6 , 9euro-a0a1l9tdb5 , aspkw-g7xq95 , aspbc-a0a1l9u6h4 , aspbc-a0a1l9u2l4 , asptc-a0a1l9mx83 , aspgl-a0a1l9ve90 , aspve-a0a1l9pvz9 , 9euro-a0a1l9tdh3 , aspc5-a0a1r3rmn9 , aspwe-a0a1l9rlq2 , asptc-a0a1l9nby7 , aspng-a0a100i8t9 , aspc5-a0a1r3rem6 , aspbc-a0a1l9uy89 , aspa1-anee , aspa1-aneh , aspa1-acrc , aspbc-alba , aspa1-acui

Title : Comparative genomics of biotechnologically important yeasts - Riley_2016_Proc.Natl.Acad.Sci.U.S.A_113_9882
Author(s) : Riley R , Haridas S , Wolfe KH , Lopes MR , Hittinger CT , Goker M , Salamov AA , Wisecaver JH , Long TM , Calvey CH , Aerts AL , Barry KW , Choi C , Clum A , Coughlan AY , Deshpande S , Douglass AP , Hanson SJ , Klenk HP , LaButti KM , Lapidus A , Lindquist EA , Lipzen AM , Meier-Kolthoff JP , Ohm RA , Otillar RP , Pangilinan JL , Peng Y , Rokas A , Rosa CA , Scheuner C , Sibirny AA , Slot JC , Stielow JB , Sun H , Kurtzman CP , Blackwell M , Grigoriev IV , Jeffries TW
Ref : Proc Natl Acad Sci U S A , 113 :9882 , 2016
Abstract : Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.
ESTHER : Riley_2016_Proc.Natl.Acad.Sci.U.S.A_113_9882
PubMedSearch : Riley_2016_Proc.Natl.Acad.Sci.U.S.A_113_9882
PubMedID: 27535936
Gene_locus related to this paper: wicaa-a0a1e3nx95 , cybjn-a0a1e4s739 , 9asco-a0a1q2yku6 , ogapd-w1qjr8 , 9asco-a0a1e3pdp5 , lipst-a0a1e3qdq0 , 9asco-a0a1e4tg55

Title : Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities - Nagy_2016_Mol.Biol.Evol_33_959
Author(s) : Nagy LG , Riley R , Tritt A , Adam C , Daum C , Floudas D , Sun H , Yadav JS , Pangilinan J , Larsson KH , Matsuura K , Barry K , LaButti K , Kuo R , Ohm RA , Bhattacharya SS , Shirouzu T , Yoshinaga Y , Martin FM , Grigoriev IV , Hibbett DS
Ref : Molecular Biology Evolution , 33 :959 , 2016
Abstract : Evolution of lignocellulose decomposition was one of the most ecologically important innovations in fungi. White-rot fungi in the Agaricomycetes (mushrooms and relatives) are the most effective microorganisms in degrading both cellulose and lignin components of woody plant cell walls (PCW). However, the precise evolutionary origins of lignocellulose decomposition are poorly understood, largely because certain early-diverging clades of Agaricomycetes and its sister group, the Dacrymycetes, have yet to be sampled, or have been undersampled, in comparative genomic studies. Here, we present new genome sequences of ten saprotrophic fungi, including members of the Dacrymycetes and early-diverging clades of Agaricomycetes (Cantharellales, Sebacinales, Auriculariales, and Trechisporales), which we use to refine the origins and evolutionary history of the enzymatic toolkit of lignocellulose decomposition. We reconstructed the origin of ligninolytic enzymes, focusing on class II peroxidases (AA2), as well as enzymes that attack crystalline cellulose. Despite previous reports of white rot appearing as early as the Dacrymycetes, our results suggest that white-rot fungi evolved later in the Agaricomycetes, with the first class II peroxidases reconstructed in the ancestor of the Auriculariales and residual Agaricomycetes. The exemplars of the most ancient clades of Agaricomycetes that we sampled all lack class II peroxidases, and are thus concluded to use a combination of plesiomorphic and derived PCW degrading enzymes that predate the evolution of white rot.
ESTHER : Nagy_2016_Mol.Biol.Evol_33_959
PubMedSearch : Nagy_2016_Mol.Biol.Evol_33_959
PubMedID: 26659563
Gene_locus related to this paper: 9homo-a0a164swv2 , 9homo-a0a164tl22 , 9homo-a0a164vkv1 , 9homo-a0a164y4j9 , 9homo-a0a164y4l9 , 9homo-a0a164ytj2 , 9homo-a0a164zeu0 , exigl-a0a165as65 , exigl-a0a165ck85 , 9basi-a0a165cm83 , 9aphy-a0a165dbf1 , 9aphy-a0a165dbf3 , 9basi-a0a165dcb7 , 9aphy-a0a165ddj9 , exigl-a0a165dj22 , exigl-a0a165dmd7 , 9aphy-a0a165egr5 , 9basi-a0a165ekd3 , 9basi-a0a165enc9 , 9basi-a0a165end6 , 9basi-a0a165epz3 , 9basi-a0a165eq46 , 9basi-a0a165eq95 , 9basi-a0a165eqk7 , 9basi-a0a165eup2 , 9aphy-a0a165fb02 , 9aphy-a0a165fmr9 , 9aphy-a0a165g3p1 , 9basi-a0a165g673 , 9basi-a0a165g6g2 , 9aphy-a0a165gec2 , 9basi-a0a165gfp7 , 9aphy-a0a165h505 , 9aphy-a0a165hd72 , 9aphy-a0a165hrk1 , exigl-a0a165hzc8 , 9basi-a0a165i2y7 , 9basi-a0a165iru3 , 9basi-a0a165is19 , 9basi-a0a165is40 , exigl-a0a165j2r4 , exigl-a0a165j754 , 9basi-a0a165jg92 , 9basi-a0a165jgb0 , exigl-a0a165ke04 , exigl-a0a165kpb0 , exigl-a0a165l7g6 , 9aphy-a0a165lux8 , 9aphy-a0a165luy2.1 , 9aphy-a0a165luy2.2 , exigl-a0a165m310 , 9aphy-a0a165mxa5 , 9aphy-a0a165mxc8 , 9aphy-a0a165mxe4 , exigl-a0a165mz73 , 9homo-a0a165nfz4 , 9homo-a0a165ng04 , 9aphy-a0a165nry3 , 9homo-a0a165ntf3 , 9homo-a0a165p2a0 , 9aphy-a0a165ph74 , 9homo-a0a165phz5 , exigl-a0a165pm12 , exigl-a0a165pu90 , exigl-a0a165puh2 , 9aphy-a0a165q9t4 , 9homo-a0a165qeb7 , 9homo-a0a165qeh8 , 9aphy-a0a165qqm2 , 9aphy-a0a165quj0 , 9aphy-a0a165qul3 , exigl-a0a165qxy0 , 9aphy-a0a165r6t2 , 9aphy-a0a165r8g4 , 9aphy-a0a165tfc7 , 9homo-a0a165tgm2 , 9homo-a0a165tzv4 , 9homo-a0a165tzw4 , 9homo-a0a165uez3 , 9homo-a0a165ugh4 , 9homo-a0a165ugp4 , 9homo-a0a165ugq6 , 9homo-a0a165uh51 , 9aphy-a0a165umj9 , 9homo-a0a165us14 , 9homo-a0a165xi11 , 9homo-a0a165xmw5 , 9homo-a0a165xmx9 , 9homo-a0a165xsk7 , 9homo-a0a165y3k8 , 9homo-a0a165yhg3 , 9homo-a0a165ymb3 , 9homo-a0a165yt77 , 9homo-a0a165ytu4 , 9homo-a0a165zr30 , 9homo-a0a166a1g9 , 9homo-a0a166a1h1 , exigl-a0a166abe4 , 9homo-a0a166akq6 , exigl-a0a166al33 , 9homo-a0a166arm1 , 9homo-a0a166as45 , 9homo-a0a166as65 , 9homo-a0a166as77 , exigl-a0a166auh4 , 9homo-a0a166azk8 , exigl-a0a166azz6 , 9homo-a0a166bss2 , 9homo-a0a166bsu9 , 9homo-a0a166bui6 , 9homo-a0a166crl5 , 9homo-a0a166d8q4 , 9homo-a0a166dss7 , 9homo-a0a166dtg8 , 9homo-a0a166du49 , 9homo-a0a166du64 , 9homo-a0a166e1z2 , 9homo-a0a166eec5 , 9homo-a0a166eux5 , 9homo-a0a166evw5 , 9homo-a0a166ey75 , 9homo-a0a166eyq0 , 9homo-a0a166ez78 , 9homo-a0a166eze7 , 9homo-a0a166fh25 , 9homo-a0a166g4k8 , 9homo-a0a166gct1 , 9homo-a0a166gf56 , 9homo-a0a166gsr8 , 9homo-a0a166j6i1 , 9homo-a0a166jiu0 , 9homo-a0a166jr36 , 9homo-a0a166kia8 , 9homo-a0a166ks21 , 9homo-a0a166kvn8 , 9homo-a0a166kxf0 , 9homo-a0a166kxg2 , 9homo-a0a166lcs7 , 9homo-a0a166lw48 , 9homo-a0a166lyz4 , 9homo-a0a166puu7.1 , 9homo-a0a166puu7.2 , 9homo-a0a166puz0 , 9homo-a0a166pv75 , 9homo-a0a166pva0 , 9homo-a0a166pvf7 , 9homo-a0a166px11 , 9homo-a0a166q635 , 9basi-a0a167gl88 , 9basi-a0a167gl97 , 9basi-a0a167gla5 , 9basi-a0a167hca0 , 9basi-a0a167hrt3 , 9basi-a0a167hru7 , 9basi-a0a167k219 , 9basi-a0a167k232 , 9basi-a0a167k265 , 9basi-a0a167l6m6 , 9basi-a0a167lrl7 , 9basi-a0a167lt70 , 9basi-a0a167mtk7 , 9basi-a0a167n1z0 , 9basi-a0a167p9x5 , 9basi-a0a167qks1 , 9basi-a0a167qkt4 , 9basi-a0a167qky5 , 9basi-a0a167qln8 , 9basi-a0a167rpp7 , 9homo-a0a167u8e3 , 9homo-a0a167v1m8 , 9homo-a0a166hqx0 , 9homo-a0a166l842 , exigl-a0a165n4f2 , exigl-a0a165q512 , 9agam-a0a165nq75 , 9agam-a0a166cv75 , 9agam-a0a165mvt4 , 9agam-a0a164t8q2 , 9agam-a0a166flp0

Title : The genome of Xylona heveae provides a window into fungal endophytism - Gazis_2016_Fungal.Biol_120_26
Author(s) : Gazis R , Kuo A , Riley R , LaButti K , Lipzen A , Lin J , Amirebrahimi M , Hesse CN , Spatafora JW , Henrissat B , Hainaut M , Grigoriev IV , Hibbett DS
Ref : Fungal Biol , 120 :26 , 2016
Abstract : Xylona heveae has only been isolated as an endophyte of rubber trees. In an effort to understand the genetic basis of endophytism, we compared the genome contents of X. heveae and 36 other Ascomycota with diverse lifestyles and nutritional modes. We focused on genes that are known to be important in the host-fungus interaction interface and that presumably have a role in determining the lifestyle of a fungus. We used phylogenomic data to infer the higher-level phylogenetic position of the Xylonomycetes, and mined ITS sequences to explore its taxonomic and ecological diversity. The X. heveae genome contains a low number of enzymes needed for plant cell wall degradation, suggesting that Xylona is a highly adapted specialist and likely dependent on its host for survival. The reduced repertoire of carbohydrate active enzymes could reflect an adaptation to intercellulary growth and to the avoidance of the host's immune system, suggesting that Xylona has a strictly endophytic lifestyle. Phylogenomic data resolved the position of Xylonomycetes as sister to Lecanoromycetes and Eurotiomycetes and placed the beetle-endosymbiont Symbiotaphrina as a member of this class. ITS data revealed that Trinosporium is also part of the Xylonomycetes, extending the taxonomic and ecological diversity of this group.
ESTHER : Gazis_2016_Fungal.Biol_120_26
PubMedSearch : Gazis_2016_Fungal.Biol_120_26
PubMedID: 26693682
Gene_locus related to this paper: 9pezi-a0a165f9w1 , 9pezi-a0a165fsb2 , 9pezi-a0a165gpf2 , 9pezi-a0a164zp96 , xylht-a0a165aju9 , xylht-a0a165jye6 , xylht-a0a165jir4

Title : Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii - Floudas_2015_Fungal.Genet.Biol_76_78
Author(s) : Floudas D , Held BW , Riley R , Nagy LG , Koehler G , Ransdell AS , Younus H , Chow J , Chiniquy J , Lipzen A , Tritt A , Sun H , Haridas S , LaButti K , Ohm RA , Kues U , Blanchette RA , Grigoriev IV , Minto RE , Hibbett DS
Ref : Fungal Genet Biol , 76 :78 , 2015
Abstract : Wood decay mechanisms in Agaricomycotina have been traditionally separated in two categories termed white and brown rot. Recently the accuracy of such a dichotomy has been questioned. Here, we present the genome sequences of the white-rot fungus Cylindrobasidium torrendii and the brown-rot fungus Fistulina hepatica both members of Agaricales, combining comparative genomics and wood decay experiments. C. torrendii is closely related to the white-rot root pathogen Armillaria mellea, while F. hepatica is related to Schizophyllum commune, which has been reported to cause white rot. Our results suggest that C. torrendii and S. commune are intermediate between white-rot and brown-rot fungi, but at the same time they show characteristics of decay that resembles soft rot. Both species cause weak wood decay and degrade all wood components but leave the middle lamella intact. Their gene content related to lignin degradation is reduced, similar to brown-rot fungi, but both have maintained a rich array of genes related to carbohydrate degradation, similar to white-rot fungi. These characteristics appear to have evolved from white-rot ancestors with stronger ligninolytic ability. F. hepatica shows characteristics of brown rot both in terms of wood decay genes found in its genome and the decay that it causes. However, genes related to cellulose degradation are still present, which is a plesiomorphic characteristic shared with its white-rot ancestors. Four wood degradation-related genes, homologs of which are frequently lost in brown-rot fungi, show signs of pseudogenization in the genome of F. hepatica. These results suggest that transition toward a brown-rot lifestyle could be an ongoing process in F. hepatica. Our results reinforce the idea that wood decay mechanisms are more diverse than initially thought and that the dichotomous separation of wood decay mechanisms in Agaricomycotina into white rot and brown rot should be revisited.
ESTHER : Floudas_2015_Fungal.Genet.Biol_76_78
PubMedSearch : Floudas_2015_Fungal.Genet.Biol_76_78
PubMedID: 25683379
Gene_locus related to this paper: 9agar-a0a0d6zyq5 , 9agar-a0a0d7a2p9 , 9agar-a0a0d7a2v2 , 9agar-a0a0d7abt2 , 9agar-a0a0d7acd3 , 9agar-a0a0d7acx0 , 9agar-a0a0d7acx9 , 9agar-a0a0d7adg2 , 9agar-a0a0d7a6d0 , 9agar-a0a0d7aen7 , 9agar-a0a0d7aez7 , 9agar-a0a0d7ahq5 , 9agar-a0a0d7akr6 , 9agar-a0a0d7al29 , 9agar-a0a0d7an16 , 9agar-a0a0d7ann7 , 9agar-a0a0d7anv1 , 9homo-a0a0d7atv2 , 9homo-a0a0d7ay28 , 9homo-a0a0d7ayz7 , 9homo-a0a0d7b1w8 , 9homo-a0a0d7b2p0 , 9homo-a0a0d7b4n4 , 9homo-a0a0d7b624 , 9homo-a0a0d7b7r3 , 9homo-a0a0d7b7w3 , 9homo-a0a0d7bac5 , 9homo-a0a0d7bav7 , 9homo-a0a0d7bbx7 , 9homo-a0a0d7bdn7 , 9homo-a0a0d7bgj9 , 9homo-a0a0d7biw2 , 9homo-a0a0d7bqi1 , 9homo-a0a0d7bv80 , 9agar-a0a0d7b6f6 , 9agar-a0a0d7b976 , 9agar-a0a0d7aeu9 , 9agar-a0a0d7ag53 , 9agar-a0a0d7b8a5

Title : Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus - Couturier_2015_Biotechnol.Biofuels_8_216
Author(s) : Couturier M , Navarro D , Chevret D , Henrissat B , Piumi F , Ruiz-Duenas FJ , Martinez AT , Grigoriev IV , Riley R , Lipzen A , Berrin JG , Master ER , Rosso MN
Ref : Biotechnol Biofuels , 8 :216 , 2015
Abstract : BACKGROUND: White-rot basidiomycete fungi are potent degraders of plant biomass, with the ability to mineralize all lignocellulose components. Recent comparative genomics studies showed that these fungi use a wide diversity of enzymes for wood degradation. Deeper functional analyses are however necessary to understand the enzymatic mechanisms leading to lignocellulose breakdown. The Polyporale fungus Pycnoporus coccineus BRFM310 grows well on both coniferous and deciduous wood. In the present study, we analyzed the early response of the fungus to softwood (pine) and hardwood (aspen) feedstocks and tested the effect of the secreted enzymes on lignocellulose deconstruction. RESULTS: Transcriptomic and proteomic analyses revealed that P. coccineus grown separately on pine and aspen displayed similar sets of transcripts and enzymes implicated in lignin and polysaccharide degradation. In particular, the expression of lignin-targeting oxidoreductases, such as manganese peroxidases, increased upon cultivation on both woods. The sets of enzymes secreted during growth on both pine and aspen were more efficient in saccharide release from pine than from aspen, and characterization of the residual solids revealed polysaccharide conversion on both pine and aspen fiber surfaces. CONCLUSION: The combined analysis of soluble sugars and solid residues showed the suitability of P. coccineus secreted enzymes for softwood degradation. Analyses of solubilized products and residual surface chemistries of enzyme-treated wood samples pointed to differences in fiber penetration by different P. coccineus secretomes. Accordingly, beyond the variety of CAZymes identified in P. coccineus genome, transcriptome and secretome, we discuss several parameters such as the abundance of manganese peroxidases and the potential role of cytochrome P450s and pectin degradation on the efficacy of fungi for softwood conversion.
ESTHER : Couturier_2015_Biotechnol.Biofuels_8_216
PubMedSearch : Couturier_2015_Biotechnol.Biofuels_8_216
PubMedID: 26692083
Gene_locus related to this paper: pycco-a0a1y2inc6 , pycco-a0a1y2ib15 , pycco-a0a1y2j2i8 , pycco-a0a1y2i5q8 , pycco-a0a1y2ib37

Title : Genomic adaptations of the halophilic Dead Sea filamentous fungus Eurotium rubrum - Kis-Papo_2014_Nat.Commun_5_3745
Author(s) : Kis-Papo T , Weig AR , Riley R , Persoh D , Salamov A , Sun H , Lipzen A , Wasser SP , Rambold G , Grigoriev IV , Nevo E
Ref : Nat Commun , 5 :3745 , 2014
Abstract : The Dead Sea is one of the most hypersaline habitats on Earth. The fungus Eurotium rubrum (Eurotiomycetes) is among the few species able to survive there. Here we highlight its adaptive strategies, based on genome analysis and transcriptome profiling. The 26.2 Mb genome of E. rubrum shows, for example, gains in gene families related to stress response and losses with regard to transport processes. Transcriptome analyses under different salt growth conditions revealed, among other things differentially expressed genes encoding ion and metabolite transporters. Our findings suggest that long-term adaptation to salinity requires cellular and metabolic responses that differ from short-term osmotic stress signalling. The transcriptional response indicates that halophilic E. rubrum actively counteracts the salinity stress. Many of its genes encode for proteins with a significantly higher proportion of acidic amino acid residues. This trait is characteristic of the halophilic prokaryotes as well, supporting the theory of convergent evolution under extreme hypersaline stress.
ESTHER : Kis-Papo_2014_Nat.Commun_5_3745
PubMedSearch : Kis-Papo_2014_Nat.Commun_5_3745
PubMedID: 24811710
Gene_locus related to this paper: 9euro-a0a017sa42 , 9euro-a0a017s0c9 , 9euro-a0a017s186 , 9euro-a0a017s8c9 , 9euro-a0a017s6r6

Title : Analysis of the Phlebiopsis gigantea genome, transcriptome and secretome provides insight into its pioneer colonization strategies of wood - Hori_2014_PLoS.Genet_10_e1004759
Author(s) : Hori C , Ishida T , Igarashi K , Samejima M , Suzuki H , Master E , Ferreira P , Ruiz-Duenas FJ , Held B , Canessa P , Larrondo LF , Schmoll M , Druzhinina IS , Kubicek CP , Gaskell JA , Kersten P , St John F , Glasner J , Sabat G , Splinter BonDurant S , Syed K , Yadav J , Mgbeahuruike AC , Kovalchuk A , Asiegbu FO , Lackner G , Hoffmeister D , Rencoret J , Gutierrez A , Sun H , Lindquist E , Barry K , Riley R , Grigoriev IV , Henrissat B , Kues U , Berka RM , Martinez AT , Covert SF , Blanchette RA , Cullen D
Ref : PLoS Genet , 10 :e1004759 , 2014
Abstract : Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high content of extractives, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine wood. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of wood extractives were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea's extractives metabolism. These results contribute to our fundamental understanding of pioneer colonization of conifer wood and provide insight into the diverse chemistries employed by fungi in carbon cycling processes.
ESTHER : Hori_2014_PLoS.Genet_10_e1004759
PubMedSearch : Hori_2014_PLoS.Genet_10_e1004759
PubMedID: 25474575
Gene_locus related to this paper: phlgi-a0a0c3nds0 , phlgi-a0a0c3niq6 , phlgi-a0a0c3pc91 , phlgi-a0a0c3pv58 , phlgi-a0a0c3rra0 , phlgi-a0a0c3rvc4 , phlgi-a0a0c3rvu0 , phlgi-a0a0c3s394 , phlgi-a0a0c3s606 , phlgi-a0a0c3s673 , phlgi-a0a0c3s8d3 , phlgi-a0a0c3sce4 , phlgi-a0a0c3sdt8

Title : Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot\/brown-rot paradigm for wood decay fungi - Riley_2014_Proc.Natl.Acad.Sci.U.S.A_111_9923
Author(s) : Riley R , Salamov AA , Brown DW , Nagy LG , Floudas D , Held BW , Levasseur A , Lombard V , Morin E , Otillar R , Lindquist EA , Sun H , LaButti KM , Schmutz J , Jabbour D , Luo H , Baker SE , Pisabarro AG , Walton JD , Blanchette RA , Henrissat B , Martin F , Cullen D , Hibbett DS , Grigoriev IV
Ref : Proc Natl Acad Sci U S A , 111 :9923 , 2014
Abstract : Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white-rot/brown-rot classification paradigm, we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically informed principal-components analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white-rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown-rot fungi. Our results suggest a continuum rather than a dichotomy between the white-rot and brown-rot modes of wood decay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.
ESTHER : Riley_2014_Proc.Natl.Acad.Sci.U.S.A_111_9923
PubMedSearch : Riley_2014_Proc.Natl.Acad.Sci.U.S.A_111_9923
PubMedID: 24958869
Gene_locus related to this paper: pleos-a0a067nlj6 , 9agar-a0a067t0n0 , 9agar-a0a067sha0 , 9homo-a0a067pav0 , pleos-a0a067n337 , 9homo-a0a067pz82 , 9homo-a0a067m7p7 , pleos-a0a067p245 , 9homo-a0a067lrz6 , 9homo-a0a067m4r5 , 9homo-a0a067mr63 , 9homo-a0a067mrq8 , 9agar-a0a067t4j6 , 9homo-a0a067pdz2 , 9homo-a0a067q2n9 , 9agar-a0a067tsx5 , 9homo-a0a067mfq5 , 9homo-a0a067qc90 , pleos-a0a067p113 , 9homo-a0a067pwi6 , 9agar-a0a067s6d7 , 9agar-a0a067tie7 , pleos-a0a067ngc3 , 9agar-a0a067st69 , 9agar-a0a067t6h9 , 9agar-a0a067tj80 , pleos-a0a067npl2 , 9agar-a0a067sm07 , 9agar-a0a067tar9 , 9agar-a0a067tid6 , 9agar-a0a067u335 , pleos-a0a067ndv5 , pleos-a0a067nqw6 , 9homo-a0a067pkj2 , 9agar-a0a067t683 , 9homo-a0a067mgl1 , 9agar-a0a067sg35 , 9homo-a0a067q7g6 , 9agar-a0a067tub0 , 9agar-a0a067t8f5 , 9agar-a0a067tj19 , 9homo-a0a067pyu9 , 9agar-a0a067tjp8 , 9agar-a0a067sjg9 , 9agar-a0a067u0h4 , pleos-a0a067nxe9 , 9agar-a0a067sqt2 , 9agar-a0a067tgx3 , 9homo-a0a067psv8 , 9agar-a0a067sq58 , 9homo-a0a067m4m0 , 9agar-a0a067tqz5 , pleos-a0a067new9 , 9homo-a0a067m9v3 , 9agar-a0a067tlx5 , 9agar-a0a067tfq4 , pleos-a0a067nln4 , pleos-a0a067ndf5 , pleos-a0a067nn26 , pleos-a0a067nfv2 , 9homo-a0a067pnd3 , 9agar-a0a067sw48 , pleos-a0a067neg3 , pleos-a0a067nz51 , pleos-a0a067naf9 , pleos-a0a067nad7 , 9agar-a0a067sxe2 , 9agar-a0a067slu3 , pleos-a0a067n7p8 , pleos-a0a067nl60 , pleos-a0a067ncd0 , 9agar-a0a067th99 , 9agar-a0a067sp22 , pleos-a0a067pbw7 , 9homo-a0a067q916 , 9homo-a0a067pwe5 , galm3-a0a067scb0 , galm3-popa

Title : Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis - Tisserant_2013_Proc.Natl.Acad.Sci.U.S.A_110_20117
Author(s) : Tisserant E , Malbreil M , Kuo A , Kohler A , Symeonidi A , Balestrini R , Charron P , Duensing N , Frei dit Frey N , Gianinazzi-Pearson V , Gilbert LB , Handa Y , Herr JR , Hijri M , Koul R , Kawaguchi M , Krajinski F , Lammers PJ , Masclaux FG , Murat C , Morin E , Ndikumana S , Pagni M , Petitpierre D , Requena N , Rosikiewicz P , Riley R , Saito K , San Clemente H , Shapiro H , van Tuinen D , Becard G , Bonfante P , Paszkowski U , Shachar-Hill YY , Tuskan GA , Young JP , Sanders IR , Henrissat B , Rensing SA , Grigoriev IV , Corradi N , Roux C , Martin F
Ref : Proc Natl Acad Sci U S A , 110 :20117 , 2013
Abstract : The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but this genomic organization has been questioned. Here we introduce the 153-Mb haploid genome of Rhizophagus irregularis and its repertoire of 28,232 genes. The observed low level of genome polymorphism (0.43 SNP per kb) is not consistent with the occurrence of multiple, highly diverged genomes. The expansion of mating-related genes suggests the existence of cryptic sex-related processes. A comparison of gene categories confirms that R. irregularis is close to the Mucoromycotina. The AMF obligate biotrophy is not explained by genome erosion or any related loss of metabolic complexity in central metabolism, but is marked by a lack of genes encoding plant cell wall-degrading enzymes and of genes involved in toxin and thiamine synthesis. A battery of mycorrhiza-induced secreted proteins is expressed in symbiotic tissues. The present comprehensive repertoire of R. irregularis genes provides a basis for future research on symbiosis-related mechanisms in Glomeromycota.
ESTHER : Tisserant_2013_Proc.Natl.Acad.Sci.U.S.A_110_20117
PubMedSearch : Tisserant_2013_Proc.Natl.Acad.Sci.U.S.A_110_20117
PubMedID: 24277808
Gene_locus related to this paper: rhiid-u9u175 , rhiid-u9trg1 , rhiid-u9uh96 , rhiid-u9ttu4

Title : The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction - Padamsee_2012_Fungal.Genet.Biol_49_217
Author(s) : Padamsee M , Kumar TK , Riley R , Binder M , Boyd A , Calvo AM , Furukawa K , Hesse C , Hohmann S , James TY , LaButti K , Lapidus A , Lindquist E , Lucas S , Miller K , Shantappa S , Grigoriev IV , Hibbett DS , McLaughlin DJ , Spatafora JW , Aime MC
Ref : Fungal Genet Biol , 49 :217 , 2012
Abstract : Wallemia (Wallemiales, Wallemiomycetes) is a genus of xerophilic Fungi of uncertain phylogenetic position within Basidiomycota. Most commonly found as food contaminants, species of Wallemia have also been isolated from hypersaline environments. The ability to tolerate environments with reduced water activity is rare in Basidiomycota. We sequenced the genome of W. sebi in order to understand its adaptations for surviving in osmotically challenging environments, and we performed phylogenomic and ultrastructural analyses to address its systematic placement and reproductive biology. W. sebi has a compact genome (9.8 Mb), with few repeats and the largest fraction of genes with functional domains compared with other Basidiomycota. We applied several approaches to searching for osmotic stress-related proteins. In silico analyses identified 93 putative osmotic stress proteins; homology searches showed the HOG (High Osmolarity Glycerol) pathway to be mostly conserved. Despite the seemingly reduced genome, several gene family expansions and a high number of transporters (549) were found that also provide clues to the ability of W. sebi to colonize harsh environments. Phylogenetic analyses of a 71-protein dataset support the position of Wallemia as the earliest diverging lineage of Agaricomycotina, which is confirmed by septal pore ultrastructure that shows the septal pore apparatus as a variant of the Tremella-type. Mating type gene homologs were identified although we found no evidence of meiosis during conidiogenesis, suggesting there may be aspects of the life cycle of W. sebi that remain cryptic.
ESTHER : Padamsee_2012_Fungal.Genet.Biol_49_217
PubMedSearch : Padamsee_2012_Fungal.Genet.Biol_49_217
PubMedID: 22326418
Gene_locus related to this paper: walsc-i4y6w1 , walmc-i4y5m3

Title : The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes - Floudas_2012_Science_336_1715
Author(s) : Floudas D , Binder M , Riley R , Barry K , Blanchette RA , Henrissat B , Martinez AT , Otillar R , Spatafora JW , Yadav JS , Aerts A , Benoit I , Boyd A , Carlson A , Copeland A , Coutinho PM , de Vries RP , Ferreira P , Findley K , Foster B , Gaskell J , Glotzer D , Gorecki P , Heitman J , Hesse C , Hori C , Igarashi K , Jurgens JA , Kallen N , Kersten P , Kohler A , Kues U , Kumar TK , Kuo A , LaButti K , Larrondo LF , Lindquist E , Ling A , Lombard V , Lucas S , Lundell T , Martin R , McLaughlin DJ , Morgenstern I , Morin E , Murat C , Nagy LG , Nolan M , Ohm RA , Patyshakuliyeva A , Rokas A , Ruiz-Duenas FJ , Sabat G , Salamov A , Samejima M , Schmutz J , Slot JC , St John F , Stenlid J , Sun H , Sun S , Syed K , Tsang A , Wiebenga A , Young D , Pisabarro A , Eastwood DC , Martin F , Cullen D , Grigoriev IV , Hibbett DS
Ref : Science , 336 :1715 , 2012
Abstract : Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.
ESTHER : Floudas_2012_Science_336_1715
PubMedSearch : Floudas_2012_Science_336_1715
PubMedID: 22745431
Gene_locus related to this paper: aurde-j0d098 , aurde-j0dc31 , glota-s7rlc1 , fompi-s8f7s4 , dacsp-m5fpg2 , dicsq-r7sm16 , dacsp-m5g7q5 , dacsp-m5fr12 , glota-s7q5w3 , fompi-s8f826.1 , fompi-s8f826.2 , dicsq-r7sy09 , glota-s7rt87 , dicsq-r7t032 , glota-s7rym7 , fompi-s8fiv2 , dacsp-m5gda3.2 , dicsq-r7swi6 , dacsp-m5frf2 , fompi-s8ebb6 , dicsq-r7sln3 , dicsq-r7sya6 , dacsp-m5g7g1 , dicsq-r7syx7 , dicsq-r7sx57 , dacsp-m5fps7 , glota-s7pwi7 , dicsq-r7swj6 , fompi-s8ejq6 , dicsq-r7spc3 , glota-s7q258 , dacsp-m5ft65 , glota-s7q3m7 , fompi-s8dkc7 , glota-s7q1z1 , fompi-s8eqi2 , glota-s7q1z8 , fompi-s8du50 , dacsp-m5gg33 , dacsp-m5g3a7 , fompi-s8ecd7 , fompi-s8dps1 , dacsp-m5fwr0 , dicsq-r7sub7 , glota-s7q8k9 , fompi-s8ffc3 , dacsp-m5g2f9 , fompi-s8ecc2 , dacsp-m5g868 , fompi-s8f890 , dicsq-r7t1a8 , fompi-s8ebx4 , fompi-s8eb97 , glota-s7q222 , glota-s7puf0 , fompi-s8f6v9 , dacsp-m5g0z2 , dacsp-m5gdh9 , fompi-s8fb37 , dacsp-m5fy91 , glota-s7q5v6 , fompi-s8fl44 , dicsq-r7stv9 , dicsq-r7szk3 , fompi-s8epq9 , glota-s7rh56 , dacsp-m5gbt1 , punst-r7s3x9 , punst-r7s0t5 , glota-s7q312 , glota-s7rhh6 , dicsq-r7t117 , dicsq-r7slz3

Title : Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis - Fernandez-Fueyo_2012_Proc.Natl.Acad.Sci.U.S.A_109_5458
Author(s) : Fernandez-Fueyo E , Ruiz-Duenas FJ , Ferreira P , Floudas D , Hibbett DS , Canessa P , Larrondo LF , James TY , Seelenfreund D , Lobos S , Polanco R , Tello M , Honda Y , Watanabe T , Ryu JS , Kubicek CP , Schmoll M , Gaskell J , Hammel KE , St John FJ , Vanden Wymelenberg A , Sabat G , Splinter BonDurant S , Syed K , Yadav JS , Doddapaneni H , Subramanian V , Lavin JL , Oguiza JA , Perez G , Pisabarro AG , Ramirez L , Santoyo F , Master E , Coutinho PM , Henrissat B , Lombard V , Magnuson JK , Kues U , Hori C , Igarashi K , Samejima M , Held BW , Barry KW , LaButti KM , Lapidus A , Lindquist EA , Lucas SM , Riley R , Salamov AA , Hoffmeister D , Schwenk D , Hadar Y , Yarden O , de Vries RP , Wiebenga A , Stenlid J , Eastwood D , Grigoriev IV , Berka RM , Blanchette RA , Kersten P , Martinez AT , Vicuna R , Cullen D
Ref : Proc Natl Acad Sci U S A , 109 :5458 , 2012
Abstract : Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little cellulose degradation. To investigate the basis for selective ligninolysis, we conducted comparative genome analysis of C. subvermispora and P. chrysosporium. Genes encoding manganese peroxidase numbered 13 and five in C. subvermispora and P. chrysosporium, respectively. In addition, the C. subvermispora genome contains at least seven genes predicted to encode laccases, whereas the P. chrysosporium genome contains none. We also observed expansion of the number of C. subvermispora desaturase-encoding genes putatively involved in lipid metabolism. Microarray-based transcriptome analysis showed substantial up-regulation of several desaturase and MnP genes in wood-containing medium. MS identified MnP proteins in C. subvermispora culture filtrates, but none in P. chrysosporium cultures. These results support the importance of MnP and a lignin degradation mechanism whereby cleavage of the dominant nonphenolic structures is mediated by lipid peroxidation products. Two C. subvermispora genes were predicted to encode peroxidases structurally similar to P. chrysosporium lignin peroxidase and, following heterologous expression in Escherichia coli, the enzymes were shown to oxidize high redox potential substrates, but not Mn(2+). Apart from oxidative lignin degradation, we also examined cellulolytic and hemicellulolytic systems in both fungi. In summary, the C. subvermispora genetic inventory and expression patterns exhibit increased oxidoreductase potential and diminished cellulolytic capability relative to P. chrysosporium.
ESTHER : Fernandez-Fueyo_2012_Proc.Natl.Acad.Sci.U.S.A_109_5458
PubMedSearch : Fernandez-Fueyo_2012_Proc.Natl.Acad.Sci.U.S.A_109_5458
PubMedID: 22434909
Gene_locus related to this paper: cers8-m2r3x2 , cers8-m2qf37 , cers8-m2pcy7 , cers8-m2pcz3 , cers8-m2qn26 , cers8-m2r654 , cers8-m2r8g9 , cers8-m2ps90 , cers8-m2qn44 , cers8-m2q837 , cers8-m2pjy6 , cers8-m2r609 , cers8-m2qy35 , cers8-m2r1n1 , cers8-m2rl22 , cers8-m2qkx5 , cers8-m2qib7 , cers8-m2rgs8 , cers8-m2rlx6 , cers8-m2r4p3 , cers8-m2rf62 , cers8-m2qyx5 , cers8-m2pcz2 , cers8-m2rm22 , cers8-m2qwb7 , cers8-m2r9u3 , cers8-m2pp23 , cers8-m2r613 , cers8-m2rup8 , cers8-m2piv7 , cers8-m2rch3 , cers8-m2qvf7 , cers8-m2qvb7 , cers8-m2qvb2 , cers8-m2pip7 , cers8-m2rb73 , cers8-m2qgd3 , cers8-m2rcg8 , cers8-m2rb68

Title : Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma - Ellison_2011_Genetics_189_55
Author(s) : Ellison CE , Stajich JE , Jacobson DJ , Natvig DO , Lapidus A , Foster B , Aerts A , Riley R , Lindquist EA , Grigoriev IV , Taylor JW
Ref : Genetics , 189 :55 , 2011
Abstract : A large region of suppressed recombination surrounds the sex-determining locus of the self-fertile fungus Neurospora tetrasperma. This region encompasses nearly one-fifth of the N. tetrasperma genome and suppression of recombination is necessary for self-fertility. The similarity of the N. tetrasperma mating chromosome to plant and animal sex chromosomes and its recent origin (<5 MYA), combined with a long history of genetic and cytological research, make this fungus an ideal model for studying the evolutionary consequences of suppressed recombination. Here we compare genome sequences from two N. tetrasperma strains of opposite mating type to determine whether structural rearrangements are associated with the nonrecombining region and to examine the effect of suppressed recombination for the evolution of the genes within it. We find a series of three inversions encompassing the majority of the region of suppressed recombination and provide evidence for two different types of rearrangement mechanisms: the recently proposed mechanism of inversion via staggered single-strand breaks as well as ectopic recombination between transposable elements. In addition, we show that the N. tetrasperma mat a mating-type region appears to be accumulating deleterious substitutions at a faster rate than the other mating type (mat A) and thus may be in the early stages of degeneration.
ESTHER : Ellison_2011_Genetics_189_55
PubMedSearch : Ellison_2011_Genetics_189_55
PubMedID: 21750257
Gene_locus related to this paper: neucr-90C4.300 , neucr-B19A17.360 , neucr-B23G1.090 , neucr-NCU00292.1 , neucr-NCU02679.1 , neucr-NCU04930.1 , neucr-NCU06573.1 , neucr-NCU08752.1 , neucr-NCU09575.1 , neucr-NCU10022.1 , neucr-q7s1x0 , neucr-q7s216 , neucr-q7s259 , neucr-q7s260 , neucr-q7scr4 , neut8-f8n463 , neut9-g4uk39 , neucr-f5hbr2 , neut8-f8mcp7 , neucr-q7ry64 , neucr-FAED , neut8-f8mrh8

Title : The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi - Eastwood_2011_Science_333_762
Author(s) : Eastwood DC , Floudas D , Binder M , Majcherczyk A , Schneider P , Aerts A , Asiegbu FO , Baker SE , Barry K , Bendiksby M , Blumentritt M , Coutinho PM , Cullen D , de Vries RP , Gathman A , Goodell B , Henrissat B , Ihrmark K , Kauserud H , Kohler A , LaButti K , Lapidus A , Lavin JL , Lee YH , Lindquist E , Lilly W , Lucas S , Morin E , Murat C , Oguiza JA , Park J , Pisabarro AG , Riley R , Rosling A , Salamov A , Schmidt O , Schmutz J , Skrede I , Stenlid J , Wiebenga A , Xie X , Kues U , Hibbett DS , Hoffmeister D , Hogberg N , Martin F , Grigoriev IV , Watkinson SC
Ref : Science , 333 :762 , 2011
Abstract : Brown rot decay removes cellulose and hemicellulose from wood--residual lignin contributing up to 30% of forest soil carbon--and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the "dry rot" fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota.
ESTHER : Eastwood_2011_Science_333_762
PubMedSearch : Eastwood_2011_Science_333_762
PubMedID: 21764756
Gene_locus related to this paper: serl3-f8prj2 , serl3-f8qcc4 , serl9-f8ngp6 , serl9-f8nhd7 , serl9-f8nhq9 , serl9-f8nq77 , serl9-f8nr67 , serl9-f8nrt5 , serl9-f8nvy7.1 , serl9-f8nvy7.2 , serl9-f8nvy8 , serl9-f8nxt0.1 , serl9-f8nxt0.2 , serl9-f8nzr3 , serl9-f8p0f0 , serl9-f8p6v0 , serl9-f8p015 , serl9-f8p018 , serl9-f8p386 , serl9-f8paz8 , serl9-f8pbv1 , serl9-f8pby1 , serl9-f8pc25 , serl9-f8pc39 , serl9-f8nia7 , serl3-f8pju2 , serl9-f8peh1 , serl9-nps3